Project description:Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of known genome sequence for which a plasmid has been reported.
Project description:The order <i>Methylococcales</i> constitutes the methanotrophs - bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These bacteria are significant players in the global carbon cycle and can produce value-added products from methane, such as biopolymers, biofuels, and single-cell proteins for animal feed, among others. Previous studies using single-gene phylogenies have shown inconsistencies in the currently established taxonomic structure of this group. This study aimed to determine and resolve these issues by using whole-genome sequence analyses. Phylogenomic analysis and the use of similarity indexes for genomic comparisons - average amino acid identity, digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) - were performed on 91 <i>Methylococcales</i> genomes. Results suggest the reclassification of members at the genus and species levels. Firstly, to resolve polyphyly of the genus <i>Methylomicrobium</i>, <i>Methylomicrobium alcaliphilum</i>, "<i>Methylomicrobium buryatense</i>," <i>Methylomicrobium japanense</i>, <i>Methylomicrobium kenyense</i>, and <i>Methylomicrobium pelagicum</i> are reclassified to a newly proposed genus, <i>Methylotuvimicrobium</i> gen. nov.; they are therefore renamed to <i>Methylotuvimicrobium alcaliphilum</i> comb. nov., "<i>Methylotuvimicrobium buryatense</i>" comb. nov., <i>Methylotuvimicrobium japanense</i> comb. nov., <i>Methylotuvimicrobium kenyense</i> comb. nov., and <i>Methylotuvimicrobium pelagicum</i> comb. nov., respectively. Secondly, due to the phylogenetic affinity and phenotypic similarities of <i>Methylosarcina lacus</i> with <i>Methylomicrobium agile</i> and <i>Methylomicrobium album</i>, the reclassification of the former species to <i>Methylomicrobium lacus</i> comb. nov. is proposed. Thirdly, using established same-species delineation thresholds (70% dDDH and 95% ANI), <i>Methylobacter whittenburyi</i> is proposed to be a later heterotypic synonym of <i>Methylobacter marinus</i> (89% dDDH and 99% ANI). Also, the effectively but not validly published "<i>Methylomonas denitrificans</i>" was identified as <i>Methylomonas methanica</i> (92% dDDH and 100% ANI), indicating that the former is a later heterotypic synonym of the latter. Lastly, strains MC09, R-45363, and R-45371, currently identified as <i>M. methanica</i>, each represent a putative novel species of the genus <i>Methylomonas</i> (21-35% dDDH and 74-88% ANI against <i>M. methanica</i>) and were reclassified as <i>Methylomonas</i> sp. strains. It is imperative to resolve taxonomic inconsistencies within this group, first and foremost, to avoid confusion with ecological and evolutionary interpretations in subsequent studies.
Project description:The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, M. album BG8 carries a range of gene inventories for additional carbon and nitrogen transformations but no genes for growth on multicarbon substrates or for N fixation.
Project description:Robust growth of the gammaproteobacterium Methylomicrobium buryatense strain 5G on methane makes it an attractive system for CH4-based biocatalysis. Here we present a draft genome sequence of the strain that will provide a valuable framework for metabolic engineering of the core pathways for the production of valuable chemicals from methane.
Project description:Sulfadiazine (SDZ)-degrading bacterial cultures were enriched from the topsoil layer of lysimeters that were formerly treated with manure from pigs medicated with (14)C-labeled SDZ. The loss of about 35% of the applied radioactivity after an incubation period of 3 years was attributed to CO2 release due to mineralization processes in the lysimeters. Microcosm experiments with moist soil and soil slurries originating from these lysimeters confirmed the presumed mineralization potential, and an SDZ-degrading bacterium was isolated. It was identified as Microbacterium lacus, denoted strain SDZm4. During degradation studies with M. lacus strain SDZm4 using pyrimidine-ring labeled SDZ, SDZ disappeared completely but no (14)CO2 was released during 10 days of incubation. The entire applied radioactivity (AR) remained in solution and could be assigned to 2-aminopyrimidine. In contrast, for parallel incubations but with phenyl ring-labeled SDZ, 56% of the AR was released as (14)CO2, 16% was linked to biomass, and 21% remained as dissolved, not yet identified (14)C. Thus, it was shown that M. lacus extensively mineralized and partly assimilated the phenyl moiety of the SDZ molecule while forming equimolar amounts of 2-aminopyrimidine. This partial degradation might be an important step in the complete mineralization of SDZ by soil microorganisms.
Project description:Two Gram-stain-negative, rod-shaped, gliding, catalase-positive, and facultative anaerobic strains, YLOS41T and XH07, were isolated from surface water of Yilong Lake and West Lake of Dali in Yunnan Province, respectively. Both strains were yellow-colored under light conditions and white-colored under dark conditions. The results of physiological and chemotaxonomic characterization, sequencing and phylogenetic analysis, and draft genome sequence comparison demonstrated that the two strains represented a single novel species within the genus Chryseobacterium, for which the name Chryseobacterium lacus sp. nov. is proposed. The type strain is YLOS41T (= KCTC 62352T = MCCC 1H00300T), and the second strain is XH07 (= KCTC 62993). During the cultivation process, we found that the colony color of the two strains changed from white to yellow with illumination. The study investigated the effects of light irradiation on the strain YLOS41T. Results showed that light irradiation did not affect the growth of cells but significantly increased carotenoid synthesis, which caused the change of colony color. In-depth metabolic analysis was conducted by transcriptome. The predominant changes were found for genes involved in carotenoid synthesis as protection from light damage. Based on the genome and transcriptome, we proved that strain YLOS41T possessed a complete synthetic pathway of carotenoid and speculated that the production was zeaxanthin. This was the first report of Chryseobacterium species with light-induced carotenoid synthesis. This study enhances our present knowledge on how Chryseobacterium species isolated from surface water responds to light damage.
Project description:Gramastacus lacus sp. n., is described from coastal lowlands of the Central and Mid North Coast regions of New South Wales, Australia. Gramastacus lacus has a restricted distribution in ephemeral habitats, being dependent on regular natural flooding and drying cycles, and burrows for survival during temporary dry cycles. Documented are population distributions in lowland habitats (3-48 m, a.s.l.) from Wamberal Lagoon, north along the coastal strip to Wallis Lake. The species is small, reaching a maximum weight of 7 grams and 21.3 mm OCL, and distinguished by a large male genital papilla, large raised post orbital ridges, laterally compressed carapace and elongated chelae.